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Updated Sept 30, 2016 with the shifting of Protictis to the Carnivora.

Here on this YouTube video
is a bat hanging upside-down on a branch (Fig. 1). And then it takes off and flies. At first it doesn’t go anywhere, but it is flying/hovering after the feet finally let go of the branch.

Note, like roterosaurs and birds,
the bat is also bipedal — only upside-down, so balancing on hind limbs is not an issue for bats. Hanging upside down is nearly universal in bats.

Figure 1. Is this the origin of bat flapping. From an inverted position, this bat rises to horizontal by flapping, still clinging to its perch until release and flight. Click to open video.

With bipedal birds and pterosaurs,
wings appeared to develop first as decorative ornaments and flapping appears to have developed as a secondary sexual behavior to enhance feathers, plumes, hairs, and membranes already in place.

Bats were never glitzy.
They were always dull and brown. They never developed elaborate pre-sex mating rituals. They were never visual creatures. So elaborate frills and colors never appeared on them.

Since bats hang bipedally inverted,
their forelimbs and especially their hands were free to develop into something else. In this case foldable wings. But to get there, everyone knows, there had to be transitional phases in bat evolution, each phase fully functioning and conferring a competitive or survival advantage. Those transitional phases have not been discovered yet in the fossil record, nor have they been visualized. One problem has been a lack of phylogenetic bracketing, which only reptileevolution.com has provided (Fig. 2, as far as I know). Even so this is a fairly broad bracket.

Figure 2. Chriacus and Onychonycteris nest as a sister to the undiscovered bat ancestor and a basal bat. Miniaturization was part of the transition. So was enlargement of the manus. It is still a mystery why the transitional form decided to start flapping.

Figure 4. Ptilocercus, Icaronycteris and a hypothetical transitional taxon based on the ontogenetically immature wing of the embryo Myotis. If you’re going to evolve wings it looks like you have to stop using them as hands early on. Note in the bat embryo there is little indication of inter-metacarpal muscle. That area looks identical to the web.

Chriacus did not flap. Onychonycteris did.
Both were arboreal, long-limbed mammals. The big question everyone has been wondering is the how and why for transitional taxon flapping.

In the above videowe can see the inverted bat rising to a horizontal configuration while flapping and maintaining its perch with its hind limbs. This same action could be done with smaller wings in incremental steps, with advancements originating with little to no membrane and improving to a full-fledged membrane and extended fingers.

Note,
in pre bats this would not be considered flying. Instead it might be considered rowing through the air. And, except for grounded bats, there is little to no contribution from the hind limbs in becoming airborne. Instead, they simply let go. This is in direct contrast to colugos, Ptilocercus, primates, and arboreal pre-rabbits, all of which had leaping hind limbs.

The next question is,
why would an inverted bat want to rise to a horizontal configuration when it has no intention of flying?

To get to the other branchwhen a pre-bat detected an insect on another branch. (Before it could attack flying insects, a prebat had to attack crawling insects, some of which were resting after a flight or were just crawling out of a pupae or hive.)

The above video was taken in a lab environment
with a single branch and a single bat. In the natural world of the Paleocene there would have been more branches available (perhaps a tangle of vines and branches). Rising to the horizontal by vigorous flapping would have put other branches within reach. Evidently, once bats had traded grasping hands for flapping hands with grasping thumbs, there was no turning back. A horizontal branch works better than a tree trunk in providing clearance for flapping arms/wings.

Bats are not like slow-moving colugos.
When not hibernating or resting, bats are active little engines of flight. We can imagine their unknown ancestors were also active little predators, with an unusual method for getting around. From vines and branches to open air flying, they took risks, experienced failure as they parachuted into the leaf litter, then climbed another tree to start all over again. Over time some bats found they could reach further branches by flapping faster, with larger strokes with longer fingers provided with broader membranes.

Bat flight is different than bird and pterosaur flight.According to Tian et al. 2006, “The kinematic data reveals that, at the relatively slow flight speeds considered, that the wing motion is quite complex, including a sharp retraction of the wing during the upstroke and a broad sweep of the fully extended wing during the downstroke. In some respects it is almost like the animal is “rowing” rather than flying!”

The bat wrist (carpus)
is interesting. And I’d like to know more about it than I do.

Figure 1. Bat carpus compared to that of the basal bat Onychonycteris, and two other mammals, Home and Ptilocercus. The pink bone is the pisiform. Some carpals appear to fuse in certain taxa. Note that in Homo and Ptilocercus the carpals are locked together, but rotate as a unit proximally. That is not the case with bats, which appear to have mobility within the carpals, not at the proximal articulation with the radius and ulna. On Onychonycteris digit 1 is preserved below the other digits and so is hidden in this graphic.

The wrist bones
of Homo and Ptilocercus are pretty well locked in as a unit, but a sliding joint permits movement (rotation in two axes) at the radius and ulna.

Bats appear to be different,
perhaps due to their ability of completely fold their hands (wings) against their antebrachia (radius + ulna or forearm), in the manner of birds and pterosaurs, in the plane of the wing. Above (Fig. 1) I have attempted to identify homologous bones. Please advise if any mistakes were made.

In the basal bat,Onychonycteris, the carpal bones were not locked into place. This could be a taphonomic issue with elements drifting. Or perhaps it represents an early stage in bat carpus evolution. Or both.

In the only bat carpus illustration
I could find (genus unknown), the proximal carpals appear to be fixed to the ulna and radius. The distal carpal elements appear to be loose. The metacarpals appear to overlap like Japanese fan struts. I don’t see the same proximal metacarpal expansion in the basal bat Onychonycteris.

Since bat wing claws are still present
on all of the fingers of Onychonycteris and with wrist rotation in the plane of the wing, the claws would still have been oriented toward the palmar side and thus could be used. Or if not used, this orientation of the fingers and claws provides clues to those of ancestral bats with smaller hands not yet used for flying that might have been likewise rotated 180 degrees while oriented ventrally on tree trunks and other vertical substrates.

I have asked for,
but have not yet received, the pdf for Greene 2005 listed below. I’m sure there will be more to say on this subject when that pdf comes in.

ReferencesGreene WE Jr. 2005. The development of the carpal bones in the bat. Journal of Morphology 89(3):409-422. Article first published online: 6 FEB 2005 DOI: 10.1002/jmor.1050890303

With the addition of more taxa,
the lineage of synapsids (including mammals) is filling up nicely — and a little differently than what was once thought. In 1982 TS Kemp produced this image (Fig. 1).

Figure 1. Synapsid evolution according to TS Kemp 1982.

The large reptile tree confirms many of these nestings, adds a few taxa, and subtracts Casea, which now nests with Milleretta and kin (Fig. 2).

Figure 2. The TS Kemp figure modified to reflect changes recovered by the large reptile tree. Casea is removed. It is not related to the rest of these taxa but nests with Milleretta. Therapsids appeared near the Haptodus node with Cutleria. Therapsids thereafter split into anomodonts and the rest of the clade.

Kemp (1982) produced his family tree (Fig. 1) without the aid of phylogenetic software and prior to the discovery of several key taxa. He was building on past work by Romer and Price (1940) and others before them. The large reptile tree also builds upon early work.

More links for synapsid family trees at reptileevolution.com here, here, and here.

Updated Sept 20, 2016, with better data on Protictis and more taxa added to the mammal clade.

One of the most popular blogposts here,
year after year, has been the post on bat origins back in 2011. Nothing has changed since then except for the fact that I have added a few bats and kin to the large reptile tree (Fig. 1, subset) and Protictis has moved to the Carnivora following better data.

And here (Fig. 2), for good measure are Chriacusand Onychonycteris, a bat ancestor candidate and a basal bat respectively, according to the large reptile tree.

Figure 2. Chriacus nests as a sister to the undiscovered bat ancestor. Onychonycteris was a basal bat. Miniaturization was part of the transition. So was enlargement of the manus. It is still a mystery why the transitional form decided to start flapping. Click to enlarge.

Phylogenetic miniaturization contributed to bat origins. The teeth became better adapted to insect eating. The larger scapulae and clavicles anchored larger muscles. The ulna became reduced relative to the radius and fused to it. The hands became enlarged. Membranes spanned the forelimbs and hind limbs. This is the only flapper that did not have an obvious bipedal phase.

It is still a mystery what evolutionary events spanned these two taxa. The rest has to be imagined.

A recent paper by Lautenschlager and Rauhut (2015) provided a reconstruction (Fig. 1)of the first known rauisuchid, Rauisuchus(von Huene 1942). I thought they provided it with something of a roller-coaster backbone, unlike that of more completely known rauisuchians. So, I moved the bones around on top of an established skeleton of Saurosuchus, which is another closely related rauisuchian of the same size (Fig. 1). Just a hypothesis based on a bauplan.

Figure 1. Rauisuchus reconstructed according to the baulplan of Saurosuchus (above) and as originally reconstructed (below). Click to enlarge

The large reptile tree is anchored on about 450 extinct taxa. However, more than a few (39) extant taxa are now included. Today we’ll simply delete all the extinct taxa and see what sort of tree we recover. This will demonstrate what changes to the tree topology occur without extinct taxa, and note how parts of it kind of resemble the latest DNA studies.

Figure 1. Cladogram of extant taxa, a subset of the large reptile tree that does not quite retain the original topology.Here turtles nest with archosaurs (in the absence of about 450 other taxa. Loss of resolution here is due to taxon exclusion. For instance, without Megazostrodon, the mammals lack resolution.

Rana the frog nests at the base, perhaps because it is now listed first among the taxa. Or perhaps because it is indeed primitive. Not sure, but if there are no objections?

There is loss of resolution
at the base of the Amniota, where three clades branch off: 1) mammals, 2) turtles and archosaurs and 3) lepidosaurs. This largely matches certain DNA studies, by the way, that nest turtles with archosaurs. Interesting solution to that old problem…

Within the Lepidosauromorpha (sans the turtles)
the clades largely match the large reptile tree. Sphenodontians split from Squamates and Iguania branches off from Scerloglossa thereafter.

Here (Fig. 1) the geckos are separated from the snakes. Instead, amphisbaenids nest with snakes. These ‘odd bedfellows’ appear due to taxon exclusion and loss of limbs.

Here 510 total taxa are reduced to 39, an exclusion of 92 percent. Like other smaller, more focused studies, this one demonstrates the problems they have and, by inference, the value of adding prehistoric taxa. That’s where the transitions are to be found.

The original tree topology is not quite retained.
Turtles transfer from lepidosauromorphs to archosauromorphs. The legless taxa nest together. This tree also nearly echoes DNA studies that have mammals branching off first in the absence of about a dozen taxa that precede synapsids in the large reptile tree.

Word of Warning
No one in their right mind would ever consider turtles the sister taxon to birds and crocs… Yet here they are. Sisterhood varies based on taxon inclusion. This situation is analogous to those that nest pterosaurs with archosaurs and archosauriformes and other such odd nestings.

By the way
I made comments to the recent Reeder et al. morphology + molecules study of squamates here. In short they did not include enough extinct taxa and did not recognize the large number of lepidosaurs that nest between Sphenodontia and Squamata, some of which nest as proximal basal taxa to the Squamata. Without them, the base of their tree did not have the correct roots and so the initial branching also suffered.

By default nestings
can be interesting and silly. The point behind nesting pterosaurs with turtles back then was to examine the folly behind nesting pterosaurs with archosaurs — only possible due to a similar taxon exclusion that’s been going on for at least fifteen years now, following the publication of a phylogenetic analysis that nested pterosaurs with fenestrasaurs (Peters 2000) and has been ignored ever since.

Back in the day (July 2011) with 360 taxa,
when all other taxa were removed from the lepidosauromorph side of the large reptile tree, Proganochelys, the turtle, nested with MPUM6009, the pterosaur at the base of the Sauropterygia. That’s bizarre, but interesting and hopefully enlightening by analogy to the achosaur-link question.

The three lepidosauromorphs:
the turtle, the lizard and the pterosaur, all nest together again in their own clade at the base of the Sauropterygia… in other words, nowhere near dinos, pre-dinos, parasuchians, Lagerpeton or Marasuchus. Delete Huehuecuetzpalli and Proganochelys nests with the turtle-like placodont, Henodus, as you might imagine, while the basal pterosaur bounces back to the birds. So one taxon in-between the turtle and pterosaur were needed this time to glue them together in a single clade and to trump the attraction of other candidate sisters.

Bottom line:
by including more and more taxa the large reptile tree provides more and more nesting sites, and thus the large reptile tree minimizes unwanted ‘by default’ nestings. Up to now other workers have been relying an tradition and paradigm for their taxon lists, and many of those traditions have been tested (and falsified) at reptileevolution.com. When workers base their smaller, more focused studies on a larger umbrella study, they will have greater success and greater confidence that their cladogram is a good one = with no ‘by default’ nestings.